A Bayesian Approach for Modeling Cattle Movements in the United States: Scaling up a Partially Observed Network

Networks are rarely completely observed and prediction of unobserved edges is an important problem, especially in disease spread modeling where networks are used to represent the pattern of contacts. We focus on a partially observed cattle movement network in the U.S. and present a method for scaling up to a full network based on Bayesian inference, with the aim of informing epidemic disease spread models in the United States. The observed network is a 10% state stratified sample of Interstate Certificates of Veterinary Inspection that are required for interstate movement; describing approximately 20,000 movements from 47 of the contiguous states, with origins and destinations aggregated at the county level. We address how to scale up the 10% sample and predict unobserved intrastate movements based on observed movement distances. Edge prediction based on a distance kernel is not straightforward because the probability of movement does not always decline monotonically with distance due to underlying industry infrastructure. Hence, we propose a spatially explicit model where the probability of movement depends on distance, number of premises per county and historical imports of animals. Our model performs well in recapturing overall metrics of the observed network at the node level (U.S. counties), including degree centrality and betweenness; and performs better compared to randomized networks. Kernel generated movement networks also recapture observed global network metrics, including network size, transitivity, reciprocity, and assortativity better than randomized networks. In addition, predicted movements are similar to observed when aggregated at the state level (a broader geographic level relevant for policy) and are concentrated around states where key infrastructures, such as feedlots, are common. We conclude that the method generally performs well in predicting both coarse geographical patterns and network structure and is a promising method to generate full networks that incorporate the uncertainty of sampled and unobserved contacts.     

The Marker State Space (MSS) Method for Classifying Clinical Samples

The development of accurate clinical biomarkers has been challenging in part due to the diversity between patients and diseases. One approach to account for the diversity is to use multiple markers to classify patients, based on the concept that each individual marker contributes information from its respective subclass of patients. Here we present a new strategy for developing biomarker panels that accounts for completely distinct patient subclasses. Marker State Space (MSS) defines “marker states” based on all possible patterns of high and low values among a panel of markers. Each marker state is defined as either a case state or a control state, and a sample is classified as case or control based on the state it occupies. MSS was used to define multi-marker panels that were robust in cross validation and training-set/test-set analyses and that yielded similar classification accuracy to several other classification algorithms. A three-marker panel for discriminating pancreatic cancer patients from control subjects revealed subclasses of patients based on distinct marker states. MSS provides a straightforward approach for modeling highly divergent subclasses of patients, which may be adaptable for diverse applications.     

Spatial Ecology and Resource Selection of Eastern Box Turtles

Eastern box turtles (Terrapene carolina carolina) are widely distributed throughout the eastern United States. Although once common throughout much of its distribution, the species has experienced declines in local populations. Understanding resource selection is important for the conservation of this species; however, few data exist on resource selection for eastern box turtles in the southeastern United States. We estimated home range and resource selection for 100 individual turtles in the Blue Ridge, Ridge and Valley, and Cumberland Plateau and Mountains physiographic regions in Tennessee, USA, from 2016 to 2018. We used step-selection functions to investigate eastern box turtle resource selection during May–August 2017 and May–August 2018 at 2 spatial scales. We classified vegetation type, measured vegetation composition and structure, recorded time since fire, and measured coarse woody debris abundance at 1,225 used telemetry locations and 1,225 associated available points. Home range sizes averaged 9.3 ha ± 3.0 (SE) using minimum convex polygon analysis, 8.25 ha ± 2.88 using 95% kernel density analysis, and 1.50 ha ± 0.56 using 50% kernel density analysis. Box turtles selected areas with greater visual obstruction at the 0–0.25-m level, greater amounts of 10-hour and 100-hour fuels (timelag categories used in fire-danger ratings), and greater litter depths compared to available locations. Box turtles were more likely to select areas with greater cover of brambles and coarser woody debris and were less likely to select areas with less vegetation cover. Vegetation type and time since last fire did not affect selection. Our data suggest that management activities that encourage greater understory vegetation cover, greater visual obstruction at the 0–0.25-m level, and greater bramble cover will enhance habitat quality for eastern box turtles. © 2020 The Wildlife Society.     

Early detection of Agrilus planipennis: investigations into the attractive range of the sex pheromone (3Z)-lactone

The emerald ash borer (EAB), Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), is a highly destructive primary pest of ash (Fraxinus sp., Oleaceae) trees outside of its native range. Ash is an important component of many ecosystems and its loss would be detrimental to both the economy and the environment. The present study aimed to improve our understanding of the effectiveness of green sticky prism traps baited with host kairomone and insect pheromone lures for A. planipennis and to collect data for modelling the range of attraction of the pheromone (3Z)-dodecen-12-olide [(3Z)-lactone]. Traps were deployed over a single flight season in urban locations of Ontario, Canada, with low densities of EAB. Traps were placed in pairs of trees separated by not more than 25 m. All traps contained the host kairomone, (3Z)-hexenol, with the remaining half in each pairing additionally baited with (3Z)-lactone pheromone. Both lure types were highly effective in capturing EAB, with >90% detection rates overall. However, traps baited with the lactone pheromone and host volatile lures doubled trap captures of EAB over distances of at least 25 m from the nearest traps baited with only host volatiles. Although the baseline detection rate of traps containing (3Z)-hexenol alone is not significantly reduced compared with traps containing (3Z)-lactone, the overall trap effectiveness is significantly increased when (3Z)-lactone is present. The implications for the use of (3Z)-lactone at 3 mg per septum dose in an early warning trapping system are discussed. Trap layout methods and risk-based analysis models can now be further refined by including these data about the attractive range of lures and their behaviour in different plot environments.     

S-Nitroso-N-acetylpenicillamine impregnated endotracheal tubes for prevention of ventilator-associated pneumonia

The chances of ventilator-associated pneumonia (VAP) increases 6–20 folds when an endotracheal tube (ETT) is placed in a patient. VAP is one of the most common hospital-acquired infections and comprises 86% of the nosocomial pneumonia cases. This study introduces the idea of nitric oxide-releasing ETTs (NORel-ETTs) fabricated by the incorporation of the nitric oxide (NO) donor S-nitroso-N-acetylpenicillamine (SNAP) into commercially available ETTs via solvent swelling. The impregnation of SNAP provides NO release over a 7-day period without altering the mechanical properties of the ETT. The NORel-ETTs successfully reduced the bacterial infection from a commonly found pathogen in VAP, Pseudomonas aeruginosa, by 92.72 ± 0.97% when compared with the control ETTs. Overall, this study presents the incorporation of the active release of a bactericidal agent in ETTs as an efficient strategy to prevent the risk of VAP.     

The natural place to begin: The ethnoprimatology of the Waorani

Ethnoprimatology is an important and growing discipline, studying the diverse relationships between humans and primates. However there is a danger that too great a focus on primates as important to humans may obscure the importance of other animal groups to local people. The Waorani of Amazonian Ecuador were described by Sponsel [Sponsel (1997) New World Primates: Ecology, evolution and behavior. New York: Aldine de Gruyter. p 143–165] as the “natural place” for ethnoprimatology, because of their close relationship to primates, including primates forming a substantial part of their diet. Therefore they are an ideal group in which to examine contemporary perceptions of primates in comparison to other types of animal. We examine how Waorani living in Yasuní National Park name and categorize primates and other common mammals. Although there is some evidence that the Waorani consider primates a unique group, the non‐primate kinkajou and olingo are also included as part of the group “monkeys,” and no evidence was found that primates were more important than other mammals to Waorani culture. Instead, a small number of key species, in particular the woolly monkey (Lagothrix poeppigii) and white‐lipped peccary (Tayassu pecari), were found to be both important in the diet and highly culturally salient. These results have implications for both ethnoprimatologists and those working with local communities towards broader conservation goals. Firstly, researchers should ensure that they and local communities are referring to the same animals when they use broad terms such as “monkey,” and secondly the results caution ethnoprimatologists against imposing western taxonomic groups on indigenous peoples, rather than allowing them to define themselves which species are important. Am. J. Primatol. 75:1117–1128, 2013. © 2013 The Authors. American Journal of Primatology Published by Wiley Periodicals, Inc.     

Survival and behavior of juvenile steelhead trout (Oncorhynchus mykiss) in two estuaries in Oregon, USA

Anadromous salmonids are viewed as a prized commodity and cultural symbol throughout the Pacific coast of North America. Unfortunately, several native salmonid populations are threatened or at risk of extinction. Despite this, little is known about the behavior and survival of these fish as the juveniles transition from freshwater to the ocean. Our primary objectives were to estimate survival of juvenile steelhead migrating between trapping sites and the ocean and evaluate whether survival in the estuary varies temporally (within a year) or spatially (within and between estuaries) within the same distinct population segment. We also evaluated whether flow or fork length were correlated with survival and collected information on variables that have been demonstrated to affect smolt survival in other studies to lend insight regarding differences in survival estimates between basins. We compared run timing, migration rate, survival, condition factor, age composition and time of residence in the estuary for steelhead outmigrants from each basin and measured parasite loads in outmigrating steelhead to evaluate potential differences in parasite density and parasite community between basins. In 2009, we implanted acoustic transmitters in 139 wild steelhead smolts in two small rivers on the Oregon Coast. In general, only 40–50 % of the wild steelhead smolts tagged at upstream smolt traps were detected entering the ocean. The majority of mortality occurred in the lower estuary near the ocean. Wild steelhead smolts typically spent less than 1 day in the estuary in both basins. Using similar data from previous studies in the Nehalem and Alsea basins, we showed that survival appears to be negatively correlated with flow in most releases, and in 2009 fork length was not correlated with survival. Our observations provide baseline information on factors that could influence smolt survival through the estuary as well as smolt to adult survival in these basins, and emphasize the importance of monitoring smolt survival in the estuary.